Ononis L. (Fabaceae, Papilionoideae) is a common genus in the circum-Mediterranean region. To infer phylogenetic relationships, 69 Ononis species were analyzed using plastid trnL-F and nuclear ITS DNA sequences. Trees resulting from maximum parsimony analysis and Bayesian inference provide evidence that Ononis is monophyletic but contradict the traditional subgeneric division in O. sects. Ononis and Natrix. However, many of the 22 subsections of the genus are well supported by the molecular data. Phylogenetic reconstructions indicate five major lineages within the genus, which are morphologically supported by peduncle length and flower color, characters which also confirm the polyphyly suggested for O. subsect. Reclinatae. Ononis subsects. Antiquae and Rhodanthae form a basally branching monophylum, confirming the findings of previous studies. An examination of the life strategies dominant in different clades and the climatic conditions in the habitats of the species in the light of the molecular data suggests that O. subsects. Ononis, Mauritanicae and Canariensis are secondarily perennial, with the latter two serving as examples of high altitude woodiness and insular woodiness.